test cleanup / ruff-ing

doc/conventions.md

@@ -0,0 +1,79 @@
+# PHARE Conventions
+
+### Reference document for the code base
+
+
+# Sections
+
+1. C++
+2. Python
+3. CMake
+4. Tests
+5. Etc
+
+<br/>
+
+# 1. C++
+
+## 1.1 General
+
+...
+
+
+<br/>
+
+# 2. Python
+
+## 2.1 General
+
+...
+
+## 2.2 dependencies and imports
+
+Third party depenencies are stated in the file `requirements.txt` in the project root.
+Fewer dependencies is generally better but there should be a cost/benefit assessment for adding new dependencies.
+
+### 2.2.1 Python file import structure.
+
+Generally, we want to avoid importing any dependency at the top of a python script that may rely on binary libraries.
+
+Exceptions to this are things like numpy, which are widely used and tested.
+
+Things to expressly avoid importing at the top of a python script are
+
+- h5py
+- mpi4py
+- scipy.optimize
+
+The first two are noted as they can, and will pull in system libraries such as libmpi.so and libhdf5.so, which may not be the libraries which were used during PHARE build time, this can cause issues at runtime.
+
+scipy.optimize relies on system libraries which may not be available at runtime.
+
+The gist here is to only import these libraries at function scope when you actually need them, so that python files can be imported
+or scanned for tests and not cause issues during these operations, until the functions are used at least.
+
+<br/>
+
+# 3. CMake
+
+## 3.1 General
+
+...
+
+
+<br/>
+
+# 4. Tests
+
+## 4.1 General
+
+...
+
+<br/>
+
+# 5. Etc
+
+## 5.1 General
+
+...
+

pyphare/pyphare/cpp/__init__.py

@@ -3,27 +3,10 @@
 #
 
 
-import json
-
-# continue to use override if set
-_cpp_lib_override = None
-
-
 def cpp_lib(override=None):
     import importlib
 
-    global _cpp_lib_override
-    if override is not None:
-        _cpp_lib_override = override
-    if _cpp_lib_override is not None:
-        return importlib.import_module(_cpp_lib_override)
-
-    if not __debug__:
-        return importlib.import_module("pybindlibs.cpp")
-    try:
-        return importlib.import_module("pybindlibs.cpp_dbg")
-    except ImportError:
-        return importlib.import_module("pybindlibs.cpp")
+    return importlib.import_module("pybindlibs.cpp")
 
 
 def cpp_etc_lib():
@@ -37,6 +20,8 @@ def build_config():
 
 
 def build_config_as_json():
+    import json
+
     return json.dumps(build_config())
 
 

pyphare/pyphare/pharesee/hierarchy/fromh5.py

@@ -15,7 +15,7 @@
 )
 from ...core.gridlayout import GridLayout
 from .hierarchy_utils import field_qties
-import h5py
+
 from pathlib import Path
 from pyphare.core.phare_utilities import listify
 
@@ -129,6 +129,8 @@ def h5_filename_from(diagInfo):
 
 
 def get_times_from_h5(filepath, as_float=True):
+    import h5py  # see doc/conventions.md section 2.1.1
+
     f = h5py.File(filepath, "r")
     if as_float:
         times = np.array(sorted([float(s) for s in list(f[h5_time_grp_key].keys())]))
@@ -216,6 +218,7 @@ def add_time_from_h5(hier, filepath, time, **kwargs):
     # add times to 'hier'
     # we may have a different selection box for that time as for already existing times
     # but we need to keep them, per time
+    import h5py  # see doc/conventions.md section 2.1.1
 
     h5f = h5py.File(filepath, "r")
     selection_box = kwargs.get("selection_box", None)
@@ -239,6 +242,8 @@ def add_data_from_h5(hier, filepath, time):
     if not hier.has_time(time):
         raise ValueError("time does not exist in hierarchy")
 
+    import h5py  # see doc/conventions.md section 2.1.1
+
     h5f = h5py.File(filepath, "r")
 
     # force using the hierarchy selection box at that time if existing
@@ -260,6 +265,8 @@ def new_from_h5(filepath, times, **kwargs):
     # loads all datasets from the filepath h5 file as patchdatas
     # we authorize user to pass only one selection box for all times
     # but in this case they're all the same
+    import h5py  # see doc/conventions.md section 2.1.1
+
     selection_box = kwargs.get("selection_box", [None] * len(times))
     if none_iterable(selection_box) and all_iterables(times):
         selection_box = [selection_box] * len(times)

src/python3/CMakeLists.txt

@@ -13,18 +13,6 @@ set_target_properties(cpp
 set_property(TARGET cpp PROPERTY INTERPROCEDURAL_OPTIMIZATION ${PHARE_INTERPROCEDURAL_OPTIMIZATION})
 set_property(TARGET cpp APPEND_STRING PROPERTY LINK_FLAGS " ${PHARE_LINK_FLAGS}")
 
-if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-  pybind11_add_module(cpp_dbg cpp_simulator.cpp)
-  target_link_libraries(cpp_dbg PUBLIC phare_simulator)
-  target_compile_options(cpp_dbg PRIVATE ${PHARE_WERROR_FLAGS} -DPHARE_HAS_HIGHFIVE=${PHARE_HAS_HIGHFIVE} -DPHARE_DIAG_DOUBLES=1 -DPHARE_CPP_MOD_NAME=cpp_dbg)
-  set_target_properties(cpp_dbg
-      PROPERTIES
-      LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/pybindlibs"
-  )
-  set_property(TARGET cpp_dbg PROPERTY INTERPROCEDURAL_OPTIMIZATION ${PHARE_INTERPROCEDURAL_OPTIMIZATION})
-  set_property(TARGET cpp_dbg APPEND_STRING PROPERTY LINK_FLAGS " ${PHARE_LINK_FLAGS}")
-endif (CMAKE_BUILD_TYPE STREQUAL "Debug")
-
 
 pybind11_add_module(cpp_etc cpp_etc.cpp)
 target_compile_options(cpp_etc PRIVATE ${PHARE_WERROR_FLAGS} -DPHARE_HAS_HIGHFIVE=${PHARE_HAS_HIGHFIVE})

tests/amr/data/field/refine/test_refine_field.py

@@ -5,8 +5,6 @@
 from pyphare.core.phare_utilities import refinement_ratio
 from pyphare.pharesee.hierarchy.patchdata import FieldData
 
-# in this module, we assume the refinement ratio is 2
-refinement_ratio = 2
 
 # below is a drawing  representing a 1D coarse FieldData, its ghost box and the
 # associated refined  FieldData this module aims at creating.

tests/core/data/gridlayout/allocSizes.py

@@ -9,10 +9,9 @@
 
 import os
 import sys
-
-print(sys.path)
-import gridparams
 import utilities
+import gridparams
+
 from pyphare.core import gridlayout
 
 
@@ -69,7 +68,6 @@ def main(path="./"):
 
     gl = gridlayout.GridLayout()
 
-    directions = gl.directions
     quantities = [
         "Bx",
         "By",
@@ -97,8 +95,6 @@ def main(path="./"):
     dyList = [0.0, 0.1, 0.1]
     dzList = [0.0, 0.0, 0.1]
 
-    maxNbrDim = 3
-
     baseName = "allocSizes"
 
     # out_1D = open(os.path.join(path, baseName + '_1d.txt'), 'w')

tests/core/data/gridlayout/deriv.py

@@ -1,18 +1,17 @@
 #!/usr/bin/env python
 #!coding: utf-8
 
-import numpy as np
+import os
+import sys
 import math
 import scipy.misc
-
-import sys
+import numpy as np
 
 from pyphare.core import gridlayout
-import os
-import gridparams
-import cellCenteredCoordinates
+
 import utilities
 import fieldNodeCoordinates
+import cellCenteredCoordinates
 
 
 class DerivParams(cellCenteredCoordinates.CenteredCoordParams):

tests/core/data/gridlayout/fieldNodeCoordinates.py

@@ -1,17 +1,14 @@
 #!/usr/bin/env python
 #!coding: utf-8
 
-import numpy as np
-
-# import math
 
+import os
 import sys
+import utilities
+import numpy as np
+import cellCenteredCoordinates
 
 from pyphare.core import gridlayout
-import os
-import gridparams
-import cellCenteredCoordinates
-import utilities
 
 # TODO : FieldNode coords is general case of cellCenteredCoord
 #        Which means this has to be fully refactor

tests/core/data/gridlayout/gridIndexing.py

@@ -6,15 +6,14 @@
 quantities and for all interpolation orders (1,2,3,4), in 1D, 2D and 3D.
 """
 
-import numpy as np
 
-import sys
-
-from pyphare.core import gridlayout
 import os
+import sys
 import utilities
 import gridparams
 
+from pyphare.core import gridlayout
+
 
 class IndexingParams(gridparams.GridParams):
     def __init__(self, dim, interpOrder):
@@ -94,7 +93,6 @@ def main(path="./"):
 
     gl = gridlayout.GridLayout()
 
-    directions = gl.directions
     quantities = [
         "Bx",
         "By",
@@ -122,8 +120,6 @@ def main(path="./"):
     dyList = [0.0, 0.1, 0.1]
     dzList = [0.0, 0.0, 0.1]
 
-    maxNbrDim = 3
-
     baseName = "gridIndexing"
 
     outFilenameBase = os.path.join(path, baseName)

tests/core/data/gridlayout/test_linear_combinaisons_yee.py

@@ -1,11 +1,11 @@
 #!/usr/bin/env pyhton
 #!coding: utf-8
 
-import numpy as np
-import utilities
+
 import os
 import sys
 
+
 # this script writes the following file
 # in 1D, in 2D and in 3D :
 # {dim} {interpOrder_i} ExToMoment

tests/diagnostic/__init__.py

@@ -13,7 +13,7 @@ def all_timestamps(sim):
 
 
 def dump_all_diags(pops=[], flush_every=100, timestamps=None):
-    import pyphare.pharein as ph, numpy as np
+    import pyphare.pharein as ph
 
     sim = ph.global_vars.sim
 
@@ -35,9 +35,7 @@ def dump_all_diags(pops=[], flush_every=100, timestamps=None):
         "pressure_tensor",
     ]:
         ph.FluidDiagnostics(
-            quantity=quantity,
-            write_timestamps=timestamps,
-            flush_every=flush_every,
+            quantity=quantity, write_timestamps=timestamps, flush_every=flush_every
         )
 
     for pop in pops:
@@ -59,7 +57,5 @@ def dump_all_diags(pops=[], flush_every=100, timestamps=None):
 
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(
-            quantity=quantity,
-            write_timestamps=timestamps,
-            flush_every=flush_every,
+            quantity=quantity, write_timestamps=timestamps, flush_every=flush_every
         )

tests/diagnostic/job_1d.py.in

@@ -1,14 +1,16 @@
 #!/usr/bin/env python3
 
 import pyphare.pharein as ph
-from pyphare.pharein import ElectronModel
-from tests.simulator import basicSimulatorArgs, makeBasicModel
+
 from tests.diagnostic import dump_all_diags
+from tests.simulator import basicSimulatorArgs, makeBasicModel
 
 out = "phare_outputs/diags_1d/"
-simInput = {"diag_options": {"format": "phareh5", "options": {"dir": out, "mode" : "overwrite"}}}
+simInput = {
+    "diag_options": {"format": "phareh5", "options": {"dir": out, "mode": "overwrite"}}
+}
 
-ph.Simulation(**basicSimulatorArgs(dim = 1, interp = 1, **simInput))
+ph.Simulation(**basicSimulatorArgs(dim=1, interp=1, **simInput))
 model = makeBasicModel()
-ElectronModel(closure="isothermal",Te = 0.12)
+ph.ElectronModel(closure="isothermal", Te=0.12)
 dump_all_diags(model.populations)

tests/diagnostic/job_2d.py.in

@@ -1,14 +1,16 @@
 #!/usr/bin/env python3
 
 import pyphare.pharein as ph
-from pyphare.pharein import ElectronModel
-from tests.simulator import basicSimulatorArgs, makeBasicModel
+
 from tests.diagnostic import dump_all_diags
+from tests.simulator import basicSimulatorArgs, makeBasicModel
 
 out = "phare_outputs/diags_2d/"
-simInput = {"diag_options": {"format": "phareh5", "options": {"dir": out, "mode" : "overwrite"}}}
+simInput = {
+    "diag_options": {"format": "phareh5", "options": {"dir": out, "mode": "overwrite"}}
+}
 
-ph.Simulation(**basicSimulatorArgs(dim = 2, interp = 1, **simInput))
+ph.Simulation(**basicSimulatorArgs(dim=2, interp=1, **simInput))
 model = makeBasicModel()
-ElectronModel(closure="isothermal",Te = 0.12)
+ph.ElectronModel(closure="isothermal", Te=0.12)
 dump_all_diags(model.populations)